Repression of Pumilio Protein Expression by Rbfox1 Promotes Germ Cell Differentiation

Abstract

RNA-binding Fox (Rbfox) proteins have well-established roles in regulating alternative splicing, but specific Rbfox isoforms lack nuclear localization signals and accumulate in the cytoplasm. The potential splicing-independent functions of these proteins remain unknown. Here we demonstrate that cytoplasmic Drosophila Rbfox1 regulates germ cell development and represses the translation of mRNAs containing (U)GCAUG elements within their 3'UTRs. During germline cyst differentiation, Rbfox1 targets pumilio mRNA for destabilization and translational silencing, thereby promoting germ cell development. Mis-expression of pumilio results in the formation of germline tumors, which contain cysts that break down and dedifferentiate back to single, mitotically active cells. Together, these results reveal that cytoplasmic Rbfox family members regulate the translation of specific target mRNAs. In the Drosophila ovary, this activity provides a genetic barrier that prevents germ cells from reverting back to an earlier developmental state. The finding that Rbfox proteins regulate mRNA translation has implications for Rbfox-related diseases.

Fig. 1. Identification of cytoplasmic isoforms encoded by Drosophila Rbfox1

(A) Schematic of Drosophila germline cyst differentiation. Germline stem cells (GSC) give rise to cystoblasts (CBs) that then divide four times to form 16-cell cysts. These divisions are incomplete and cells remain connected through cytoplasmic bridges called ring canals (magenta). During these divisions the fusome (green) branches (region 1 and 2A). Fusomes are specialized organelles that become increasingly more branched up until the 16-cell cyst stage, when they begin to undergo degradation (de Cuevas and Spradling, 1998). The fusome is labeled with the adducin-like protein Hu li tai shao (Hts). After germ cells complete their mitotic divisions, the fusome degrades (region 2B). Persistence of fusomes typically indicates a defect in germ cell differentiation. Cytoplasmic Sex lethal (Sxl) is expressed in GSCs and stays on until the 2-cell cyst stage. Rbfox1 is first observed in 4-cell cysts, with a peak of expression at 8-cell and Region 2A 16-cell cyst stage. Rbfox1 levels subsequently decrease. (B) Schematic of the Rbfox1 locus showing that Rbfox1-RF and Rbfox1-RN both use an alternative splice site that results in exclusion of a nuclear localization signal (NLS) contained in the other annotated isoforms. (C) A wild-type germarium stained for Rbfox1 (magenta), the fusome marker Hts (green) and DNA (blue). Regions 1, 2A, 2B and 3 are indicated. (C′) Rbfox1 staining alone. The bracket marks germ cells that express high levels of cytoplasmic Rbfox1. Small arrows mark somatic follicle cells that express nuclear Rbfox1. (D) vasa-gal4>UAS-HA::Rbfox1-RF (vasa-gal4>HA::Rbfox1-RF) germarium stained for the HA-tagged transgene (magenta) and DNA (blue). (E–F) Germaria from (E) vasa-gal4/CyO; Rbfox1^e03440/Df (vasa-gal4>Rbfox1^e03440/Df), (F) vasa-gal4>UAS-HA::Rbfox1-RF; Rbfox1^e03440/Df (vasa-gal4>HA::Rbfox1-RF; Rbfox1^e03440/Df) and (G) nanos-gal4; UAS-Rbfox1-RF^RNAi (nanos-gal4>Rbfox1-RF^RNAi) females stained for Hts (green) and DNA (blue). (H) Rbfox1^dsRed.1 homozygous mutant germarium stained for Rbfox1 (magenta), Hts (green) and DNA (blue). The bracket marks cysts that lack high levels of cytoplasmic Rbfox1. Arrows mark Rbfox1^dsRed.1 mutant somatic cells that retain nuclear Rbfox1. Scale bars represent 10 μm.

Fig. 2. Rbfox1 regulates mRNAs containing 3′UTR (U)GCAUG elements

(A) On the left panel, addition of recombinant GST-Rbfox1 RRM results in a shift of 3XUGCAUG RNA mobility that is outcompeted by non-labeled RNA. This shift is not observed with 3X UGCAUA RNA (right panel). (B) Schematic of 1X UGCAUG (1X Rbfox1 sensor), 2X UGCAUG (2X Rbfox1 sensor), 3X UGCAUG (3X Rbfox1 sensor) and 3X UGCAUA (mutant sensor) sensors. (C) IP followed by RT-PCR reveals that Rbfox1 associates with the 3X Rbfox1 sensor mRNA in vivo. (D–H) Ovaries of the indicated genotypes expressing (D) 1X Rbfox1 sensor, (E) 2X Rbfox1 sensor, (F and H) 3X Rbfox1 sensor or (G) mutant sensor stained for Venus (green) and Rbfox1 (magenta). Scale bars represent 10 μm.

Fig. 3. Rbfox1 represses Pumilio protein expression

(A) Schematic showing sequence conservation between GCAUG sites contained within the 3′UTR of pumilio genes in different Drosophila species. (B-B′) Wild-type and (C-C′) Rbfox1^dsRed.1 mutant germaria stained for Pumilio (green) and Rbfox1 (magneta). (D) Quantification of pumilio mRNA levels relative to vasa within populations of control and Rbfox1 mutant germ cells undergoing synchronous differentiation (p-value=0.0458)(see Fig. S2). (E) Western blot showing Rbfox1 and Pumilio protein expression levels within populations of control and Rbfox1 mutant germ cells as in D. (F) Quantification of the percentage of egg chambers that contain polyploid nurse cells or germ cell tumors in the indicated RNAi backgrounds (n= >100 egg chambers). (G) bam-gal4; UAS-Rbfox1-RF^RNAi; UAS-eGFP^RNAi (Rbfox1-RF^RNAi; eGFP^RNAi) and (H) bam-gal4; UAS-Rbfox1-RF^RNAi; UAS-pum^RNAi (Rbfox1-RF^RNAi; pum^RNAi) ovarioles stained for Hts (green) and DNA (magenta). (I) Schematic of pumilio 3′UTR reporters. (J-J′) Expression of the Pum GCAUG and (K-K′) Pum ACAUA mutant pumilio 3′UTR reporters (green) relative to Rbfox1 (magenta) expression. (B–C′; J–K′) Scale bars represent 10 μm. (G,H) Scale bars represent 40 μm.

Fig. 4. Expanded expression of Pumilio blocks germ cell differentiation

(A) Schematic of the UAS-full length pumilio transgenes that carry endogenous pumilio 3′UTR (pum-pum) or α-Tubulin 3′UTR (pum-Tub). (B) Quantification of the percent of egg chambers with polyploid nurse cells or germ cell tumors upon expression of the pum-pum or pum-Tub transgenes driven by germline specific vasa-gal4 driver (n= >100 egg chambers). (C) vasa-gal4 alone (control), (D) vasa-gal4>UAS-pum-pum 3′UTR (vasa-gal4>pum-pum) and (E) vasa-gal4>UAS-pum-Tub 3′UTR (vasa-gal4>pum-Tub) germaria stained for Hts (green) and Vasa (Vas) (magenta). (F) vasa-gal4 alone (control), (G) vasa-gal4>pum-pum 3′UTR and (H) vasa-gal4>pum-Tub 3′UTR germaria stained for Sxl (green) and Rbfox1 (magenta). Scale bars represent 10 μm.

Fig. 5. Germ cells dedifferentiate upon ectopic Pumilio expression

(A–B) vasa-gal4>pum-Tub 3′UTR or (C–D) Rbfox1^dsRed.1 ovaries stained for Hts (green) and galactosyl (β-1,3) N-acetylgalactosamine (magenta) (which we observe is normally enriched in ring canals) with the biotinylated lectin peanut agglutinin. Arrows point to either ring canals undergoing degradation, characteristic of cysts undergoing dedifferentiation (A-A′ and C-C′) or to remnants of ring canals after cyst have completed dedifferentiation to individual cells (B-B′ and D-D′). (E,E′) A 3D reconstruction of a Rbfox1^dsRed.1 homozygous mutant germarium stained for Hts (green). A white arrow marks the anterior (A) to posterior (P) axis. The boxed region in (E) is magnified in (E′). Yellow arrows mark fusomes in the process of breaking down. Yellow arrowheads mark round fusomes contained within single cells. (F) Normally Pumilio is expressed in GSCs and stays on until the 2-cell cyst stage where it promotes a proliferative undifferentiated state. In 4-cell cysts, Pumilio levels dramatically decrease and cytoplasmic Rbfox1 levels start to increase. During this phase, Rbfox1 directly represses pumilio expression through its 3′UTR. This promotes germline differentiation. Rbfox levels then decrease and the differentiation program continues, marked by disappearance of branched fusomes. When cells attempt to undergo differentiation in the absence of Rbfox1 (lower scheme), Pumilio levels never decrease. In turn, these germ cell cysts revert back to single cells and never reach a terminally differentiated state. (A–D) Scale bars represent 2 μm.